Fernando L. Silva

Large ionic clusters in concentrated aqueous NaCl solution

The stability of the local structure of aqueous 1.0 M NaCl solution at 293 K was investigated by molecular dynamics simulations. The mean and maximum life-times of the ion pairs were determined to be 0.13, 0.14 and 0.27 ps for negatively charged, neutral and positively charged ions pairs, respectively. The stability of non-neutral ion pairs was studied from the structure of the anion–cation radial distribution function and other structural functions. We found that non-neutral ions pairs are stabilized by at least one counter-ion forming in this way large ionic clusters that include the hydration molecules. About 25% of the ions are included in neutral clusters formed by a minimum of four ions. The existence of these large clusters obfuscates the commonly accepted chemical reaction scheme for the interconvention of ion pairs in aqueous solutions.

Multiobjective Evolutionary Algorithm With Many Tables for Purely Ab Initio Protein Structure Prediction

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment‐based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well‐designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β‐sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called “Multiobjective evolutionary algorithms with many tables” (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG, I‐PAES, and Quark) that use different levels of earlier knowledge.

Fast coarse-grained model for RNA titration

A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

Protein-RNA complexation driven by the charge regulation mechanism

Electrostatic interactions play a pivotal role in many (bio)molecular association processes. The molecular organization and function in biological systems are largely determined by these interactions from pure Coulombic contributions to more peculiar mesoscopic forces due to ion-ion correlation and proton fluctuations. The latter is a general electrostatic mechanism that gives attraction particularly at low electrolyte concentrations. This charge regulation mechanism due to titrating amino acid and nucleotides residues is discussed here in a purely electrostatic framework. By means of constant-pH Monte Carlo simulations based on a fast coarse-grained titration proton scheme, a new computer molecular model was devised to study protein-RNA interactions. The complexation between the RNA silencing suppressor p19 viral protein and the 19-bp small interfering RNA was investigated at different solution pH and salt conditions. The outcomes illustrate the importance of the charge regulation mechanism that enhances the association between these macromolecules in a similar way as observed for other protein-polyelectrolyte systems typically found in colloidal science. Due to the highly negative charge of RNA, the effect is more pronounced in this system as predicted by the Kirkwood-Shumaker theory. Our results contribute to the general physico-chemical understanding of macromolecular complexation and shed light on the extensive role of RNA in the cells life.

TRATAMENTO ELETROQUÍMICO DE EFLUENTE DA PRODUÇÃO DE BIODIESEL USANDO UM ELETRODO DO TIPO ADE: Ti/IrO2-Nb2O5

Carlos H. M. Fernandesa, Marcelo M. Yamasakia, Fernando L. Silvab, Vanessa M. Vasconcelosb, Robson S. Rochab, Marcos R. V. Lanzab,*, Marilza Castilhoa, Evandro L. Dall’Óglioa e Ailton J. Terezoa,* Departamento de Química, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa, 2367, Boa Esperança, 78090600 Cuiabá – MT, Brasil Instituto de Química de São Carlos, Universidade de São Paulo, 13560-970, São Carlos – SP, Brasil

Carbon Modified with Vanadium Nanoparticles for Hydrogen Peroxide Electrogeneration

AbstractThis paper compares the results of two preparation routes for the production of carbon (Vulcan XC 72R) modified with vanadium nanostructured electrocatalysts for hydrogen peroxide (H2O2) electrogeneration using the following mass proportions of vanadium on carbon (V/C): 1, 3, 5, 7, 10, and 13%. Best results for H2O2 electrogeneration were obtained using a V/C sol-gel method (SGM) with 3%, highest ring currents. For oxygen reduction reaction (ORR), using the V/C SGM with 3% and V/C polymeric precursor method (PPM) with 7%, the results of ring currents measured are very high when compared to Vulcan XC 72R. X-ray diffraction (XRD) analysis mainly showed the V2O5 phase. X-ray photoelectron spectroscopy (XPS) results of the V/C PPM 7% and V/C SGM 3% samples highlight the predominance of the V2O5 phase and, for the latter catalyst, a more oxidized carbon surface. For the most promising electrocatalysts, the contact angle was evaluated, showing that the anchoring of the metal in the carbon surface increases the hydrophilicity of the materials. The prepared materials are promising for peroxide electrogeneration mainly due to the synergetic effect of vanadium oxide nanoparticles and acid oxygen species of the carbon, contributing to enhancing catalyst hydrophilicity. Graphical AbstractElectrocatalytic activity toward peroxide electrogeneration using V/C electrodes